strange i have no idea what causes that. meanwhile you can use AnimatedGroup.getRoot().getTranslation() instead of getRoot().getTransformedCenter(). that seem to work correct. since root is a dummy object with no triangles its transformed center and its translation are the same.

btw, sometimes keys dont work that's why I couldnt find move key in the first time. this is a windows 8.1 machine

That's a Java focus thing (either I added KeyMapper to the frame or to the Canvas and it's supposed to be the other one). Very likely it's a Java events bug, but as long as you don't mess with the frame (just start the program and don't ALT-TAB or anything) it should always work.

For my program, I have solved the position issue by adding a child object and getting its center, but it would be nice to figure out what this issue is (and potentially solve it).

i guess there is no problem here. you set center's of root objects that's why getTranslation and getTransformedCenter return different values. that's also the reason of numeric distance is increasing when objects visually come closer.

and there is also another problem. see the screenshots. in the first the model is bind pose, in the second its animated. as you see the skeleton and the model moves somewhere else when animating. you can load your model into LoadBonesFormatSample and see yourself. so root's transformed center or translation does not reflect the actual place of the model.